This repository contains the data processing and analysis scripts for our single-cell RNA-seq and Spatial transcript (ST-seq) of skin wound healing study leaded by Liu et al..
- 01-scRNAseq Acute Wounds contains scripts and notebooks used for running CellRanger, Removing Doublets, Seurat, cell-cell crosstalk analysis, subclustering analysis of acute wounds, and Milo cell abundance analysis.
- 02-STseq Acute Wounds contains scripts used for running SpaceRanger, standard seurat analysis and plotting, and preparation for deconvolution.
- 03-Deconvolution contains scripts and notebooks used for running the deconvolution analysis of spatial data and bulk RNA-seq data based on the cell type signatures in scRNA-seq.
- 04-Data Integration contains scripts and notebooks used for integrating scRNA-seq datasets from different sources. e.g. healthy adult skin scRNA-seq, diabetic foot ulcer scRNA-seq, venous ulcer scRNA-seq, and acute wound scRNA-seq.
- 05-Cross species analysis contains scripts used for corss-species comparison of human and mouse wound healing.
- Rshiny scwoundatlas contains scripts used for creating RShiny visualization tool in our website.
- custom functions contains scripts used for common functions.
- scripts reproduce figures contains scripts used for reproducing figures in our manuscript.
Processed data can be accessed on our web portal at https://www.xulandenlab.com/tools [Not publicly available right now]
Raw requencing data for this study will be deposited in GEO: https://www.ncbi.nlm.nih.gov/geo/. Please keep an eye on our manuscript.
Feel free to post an issue in this repository or contact by email zhuang.liu[at]ki.se or ning.xu[at]ki.se if you have any questions.